algaeClassify: Tools to Standardize Phytoplankton Taxonomic Data and Perform Functional Group Classifications

Functions that facilitate the use of accepted taxonomic nomenclature, collection of functional trait data, and assignment of functional group classifications to phytoplankton species. Possible classifications include Morpho-functional group (MFG; Salmaso et al. 2015 <doi:10.1111/fwb.12520>) and CSR (Reynolds 1988; Functional morphology and the adaptive strategies of phytoplankton. In C.D. Sandgren (ed). Growth and reproductive strategies of freshwater phytoplankton, 388-433. Cambridge University Press, New York). Versions 2.0.0 and later includes new functions for querying the algaebase online taxonomic database (www.algaebase.org), however these functions require a valid API key that must be acquired from the algaebase admin. Note that none of the algaeClassify authors are affiliated with algaebase in any way. Taxonomic names can also be checked against a variety of taxonomic databases using the geographic name resolution service (GNRS) via wrapper functions for the taxize package, with convenient output format and unlikely names for phytoplankton taxa removed. In addition, currently accepted and outdated synonyms, and higher taxonomy, can be extracted for lists of species from the ITIS database using wrapper functions for the ritis package. The algaeClassify package is a product of the GEISHA (Global Evaluation of the Impacts of Storms on freshwater Habitat and Structure of phytoplankton Assemblages), funded by CESAB (Centre for Synthesis and Analysis of Biodiversity) and the USGS John Wesley Powell Center for Synthesis and Analysis, with data and other support provided by members of GLEON (Global Lake Ecology Observation Network). DISCLAIMER: This software has been approved for release by the U.S. Geological Survey (USGS). Although the software has been subjected to rigorous review, the USGS reserves the right to update the software as needed pursuant to further analysis and review. No warranty, expressed or implied, is made by the USGS or the U.S. Government as to the functionality of the software and related material nor shall the fact of release constitute any such warranty. Furthermore, the software is released on condition that neither the USGS nor the U.S. Government shall be held liable for any damages resulting from its authorized or unauthorized use.

Version: 2.0.2
Depends: R (≥ 4.3.0)
Imports: lubridate, stats, taxize, ritis, curl, jsonlite, methods, RCurl
Published: 2024-01-12
Author: Vijay Patil [aut, cre], Torsten Seltmann [aut], Nico Salmaso [aut], Orlane Anneville [aut], Marc Lajeunesse [aut], Dietmar Straile [aut]
Maintainer: Vijay Patil <vpatil at usgs.gov>
License: CC0
URL: https://doi.org/10.5066/F7S46Q3F
NeedsCompilation: no
Materials: README NEWS ChangeLog
CRAN checks: algaeClassify results

Documentation:

Reference manual: algaeClassify.pdf

Downloads:

Package source: algaeClassify_2.0.2.tar.gz
Windows binaries: r-devel: algaeClassify_2.0.2.zip, r-release: algaeClassify_2.0.2.zip, r-oldrel: algaeClassify_1.3.2.zip
macOS binaries: r-release (arm64): algaeClassify_2.0.2.tgz, r-oldrel (arm64): algaeClassify_1.3.2.tgz, r-release (x86_64): algaeClassify_2.0.2.tgz
Old sources: algaeClassify archive

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